GDM tool – Generalised Dissimilarity Modelling

A set of R functions written to perform generalized dissimilarity modelling (GDM).1

Description

Generalized dissimilarity modelling (GDM) is a statistical technique for analysing and predicting spatial patterns of turnover in community composition (beta diversity) across large regions.

The approach is an extension of matrix regression, designed specifically to accommodate two types of nonlinearity commonly encountered in large-scaled ecological data sets: (1) the curvilinear relationship between increasing ecological distance, and observed compositional dissimilarity, between sites; and (2) the variation in the rate of compositional turnover at different positions along environmental gradients.

GDM can be further adapted to accommodate special types of biological and environmental data including, for example, information on phylogenetic relationships between species and information on barriers to dispersal between geographical locations.2

Applications of generalised dissimilarity modelling.3

The GDM tool is a set of functions for performing GDM within the R statistical software environment.4

The functions are as follows:5

• gdm.fit – used to fit a generalized dissimilarity model to data provided in a site-by-species table and a corresponding table of environmental predictors for the same set of sites.
• gdm.summary – used to produce a summary of the gdm model object returned by gdm.fit.
• gdm.plot – used to plot the functions fitted to each predictor in a gdm model object returned by gdm.fit, and to produce scatter-plots of observed versus predicted dissimilarities between site-pairs.
• gdm.predict – uses a gdm model object returned by gdm.fit to predict compositional (biological) dissimilarity between pairs of sites, based on the values of environmental predictors at these sites. 
• gdm.transform – uses a gdm model object returned by gdm.fit to transform environmental data for any specified set of sites.

Developed by Simon Ferrier and Glenn Manion at NSW Department of Environment and Conservation.

Function

• Analysis tool
• User interface
  • Personal use
  • Raw data, a GIS version for visual representation is under development

Why use this tool?

GDM can be applied to a wide range of assessment activities including visualization of spatial patterns in community composition, constrained environmental classification, distributional modelling of species or community types, survey gap analysis, conservation assessment, and climate-change impact assessment.6

Who will use this tool?

• Data users
  • Expert
• Special skills are required

How will the tool be used?

• Requires R statistical package
• Requires Windows environment
• This tool is written in C-code and can be modified to be a tool for the ALA
• Desktop application
• user input required

Where in the data chain could this tool be used?

• User’s machine

When could this tool be used?

• As a post process, after data is with the user

Availability

• Download: http://www.biomaps.net.au/gdm/GDM_R_Distribution_Pack_V1.1.zip
• R statistical software: http://www.r-project.org/
• Contact: Operation - Glenn Manion: glenn.manion@environment.nsw.gov.au
• Contact: GDM approach – Simon Ferrier Simon.Ferrier@csiro.au
• Licence: Negotiate with NSW Department of Environment and Conservation

Comments

The GDM tool can be modified to sit within, and use the architecture of the ALA.7